Align Galactose/methyl galactoside import ATP-binding protein MglA; EC 7.5.2.11 (characterized)
to candidate N515DRAFT_2413 N515DRAFT_2413 simple sugar transport system ATP-binding protein
Query= SwissProt::P23924 (506 letters) >FitnessBrowser__Dyella79:N515DRAFT_2413 Length = 505 Score = 305 bits (782), Expect = 2e-87 Identities = 175/509 (34%), Positives = 291/509 (57%), Gaps = 20/509 (3%) Query: 5 ISPPSGEYLLEMRGINKSFPGVKALDNVNLNVRPHSIHALMGENGAGKSTLLKCLFGIYQ 64 +SP + +L+ RG+ K F ALD V+L +R +HALMG+NGAGKSTL+K L G+ + Sbjct: 4 VSPAARPVVLQARGLGKRFGATLALDGVDLALRAGEVHALMGQNGAGKSTLIKLLTGVER 63 Query: 65 KDSGSIVFQGKEVDFHSAKEALENGISMVHQELNLVLQRSVMDNMWLGRYPTKG--MFVD 122 D GS+ G+ + + EA +GI V+QE+NL SV +N++ GRYP + +D Sbjct: 64 PDRGSVELDGRVIAPSTPMEAQRDGIGTVYQEVNLCPNLSVAENLYAGRYPRRRRLRMID 123 Query: 123 QDKMYQDTKAIFDELDIDIDPRARVGTLSVSQMQMIEIAKAFSYNAKIVIMDEPTSSLTE 182 ++ +++ +L +++D A +G+ V+ QM+ IA+A +A+++I+DEPTSSL E Sbjct: 124 WRQVRDGARSLLRQLHLELDVDAPLGSYPVAIRQMVAIARALGVSARVLILDEPTSSLDE 183 Query: 183 KEVNHLFTIIRKLKERGCGIVYISHKMEEIFQLCDEITILRDGQWIATQPLEGLDMDKII 242 EV LF +I +L+ERG I++++H +++++ + D IT+LRDG + + L ++ Sbjct: 184 GEVRELFRVIAQLRERGMAILFVTHFLDQVYAVSDRITVLRDGCRVGEYAVADLPPAALV 243 Query: 243 AMMVGRSL-------NQRFPDKENKPGDVILEVRHLTSLRQPSIRDVSFDLHKGEILGIA 295 MVGR L +R P + P ++ + L + + V + +GE+LG+ Sbjct: 244 NAMVGRDLPTVAGADAERAPPPDAPPA---IDAQGLGC--RGKLHPVDLQVRRGEMLGLG 298 Query: 296 GLVGAKRTDIVETLFGIREKSSGTITLHGKKINNHTANEAINHGFALVTEERRSTGIYAY 355 GL+G+ RT++ LFG+ G + + G+++ +A+ G AL EER++ GI A Sbjct: 299 GLLGSGRTELARLLFGLDRAERGELRIGGERVELKHPADAVVRGLALCPEERKTDGIVAE 358 Query: 356 LDIGFNSLISNIRNYKNKVGLLDNSRMKSD--TQWVIDSMRVKTPGHRTQIGSLSGGNQQ 413 L + N +++ + + G SR + D + ++ ++ +K T +G LSGGNQQ Sbjct: 359 LSVRENIVLA----LQARQGWRGMSRARQDELARQLVQALGIKAADIETPVGLLSGGNQQ 414 Query: 414 KVIIGRWLLTQPEILMLDEPTRGIDVGAKFEIYQLIAELAKKGKGIIIISSEMPELLGIT 473 KV++ RWL+T+P +L+LDEPTRGIDV AK E+ + A G ++ IS+E EL Sbjct: 415 KVMLARWLVTEPRLLILDEPTRGIDVAAKQELMAEVTRRAHAGMAVLFISAETGELTRWC 474 Query: 474 DRILVMSNGLVSGIVDTKTTTQNEILRLA 502 DRI VM +G + +T + +A Sbjct: 475 DRIAVMRERRKAGELPGGSTEARVLAMIA 503 Lambda K H 0.319 0.137 0.388 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 535 Number of extensions: 28 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 506 Length of database: 505 Length adjustment: 34 Effective length of query: 472 Effective length of database: 471 Effective search space: 222312 Effective search space used: 222312 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory